MuRF1 Timecourse DGE report

Setup

successfully normalized  countdata

tested contrasts

successfully calculated contrasts:

QC

qc plots above

Differential expression

${regdir} regulated feature: ${num_reg}

${regdir} regulated feature: ${num_reg}

${regdir} regulated feature: ${num_reg}

${regdir} regulated feature: ${num_reg}

${regdir} regulated feature: ${num_reg}

${regdir} regulated feature: ${num_reg}

${regdir} regulated feature: ${num_reg}

${regdir} regulated feature: ${num_reg}

${regdir} regulated feature: ${num_reg}

${regdir} regulated feature: ${num_reg}

${regdir} regulated feature: ${num_reg}

${regdir} regulated feature: ${num_reg}

${regdir} regulated feature: ${num_reg}

${regdir} regulated feature: ${num_reg}

Fold Change Comparisons - Ctl vs Treatment

24h Change

24h-72h Change

0-72h Change

GO contrasts Enrichment

MT_vs_MB

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Ctrl_MT_A24_vs_MT

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Ctrl_MT_A72_vs_MT_A24

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Ctrl_MT_A72_vs_MT0

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Aspecific_MT_A24_vs_MT

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Aspecific_MT_A72_vs_MT_A24

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Aspecific_MT_A72_vs_MT0

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GO - term table

GO - GO-gene map

Output Tables

Below you can see the files into which various objects from the above analysis have been saved.

dir.create(here('tables'),showWarnings = F)

#raw count data
counts(dds)%>%as.data.frame%>%rownames_to_column('gene_id')%>%write_tsv(here('tables/rawcountdata.tsv'))
assay(normcounts)%>%as.data.frame%>%rownames_to_column('gene_id')%>%write_tsv(here('tables/normcountdata.tsv'))
#all coefficient, fold changes
resultslist%>%map_df(.id='contrast',as.data.frame)%>%write_tsv(here('tables/allcontrasts.tsv'))

# #mapping from GO terms to genes
# GTOGO%>%write_tsv(here('tables/go_gene_map.tsv'))
# #
# contrgotables%>%write_tsv(here('tables/contrast_goenrich.tsv'))